Otsutsuki Origins
by geardagum
Summary: After losing everyone in an invasion by the Otsutsuki clan, Naruto has to go all the way back to the beginning.
1. Chapter 1

**"Naruto.."**

"Quiet Kurama, I have to focus."

**"If this doesn't work.. I just want to say it was fun. Being sealed in you and getting into battle. You are one of the few humans I have actually accepted and talked to."**

"Me too."

Ever since Jigen finally used Kawaki as a vessel for one of the strongest Otsutsuki clan members to actually be alive again, the Earth was destroyed. Everyone, from Sasuke to Hinata to Boruto was dead at the hands of that retched Otsutsuki.

_"Naruto.." Sasuke began as Naruto held his dying body in his hands, "You can't keep fighting. If you do, you will die along with the rest of us, and there will be no one left to defend the rest of the innocent people who are in danger."_

_Naruto desperately tried to use his Six-Paths healing to save Sasuke, but it wasn't working; jutsu cast by a high-level Otsutsuki such as the one that was destroying Earth couldn't be affected by the likes of humans._

_"Take my eyes, Naruto." Sasuke said. He raised his hand, and with his last bit of energy, extracted his Rinnegan and put it in Naruto's hand. Sasuke's eyes closed and he took his last breath and said, "Itachi.. I finally get to see you again."_

_Tears ran from Naruto's eyes as he put down Sasuke's cold body. Out of Naruto's sleeve came a canister with Kakashi's Mangekyo Sharingan in it. One by one, Naruto replaced his eyes with more powerful ones._

_With those very eyes he saw the landscape littered with the bodies of his fallen comrades. _

_Naruto held Sasuke's body and took himself into his fallen sensei's pocket dimension along with Sasuke._

_And from there Naruto worked on a seal that would bring him back 23 years._

"Its finally complete," Naruto said as he stood up and inspected the seal. "We can finally go back in time, Kurama."

The seal was very complex, even more so than his father's Hiraishin. The paper was 20 feet in length and 20 feet wide. It was littered with time-space seals, and regular sealing.

**"Lets go then.."** Kurama muttered.

Naruto began to meditate for a long time to gain Nature energy. Nature energy was not very plentiful in the pocket dimension he was in.

Naruto pushed chakra into the seal and it began to glow. Naruto had to expend almost all of his and Kurama's chakra in order for it to work. The seal markings eventually came off of the paper and covered Naruto. He became more and more translucent until he just disappeared.

As Naruto and Kurama went through time, they saw fractals. And they saw familiar faces made out of those fractals. The seal worked by having them travel many times faster than the speed of light.

Just as fast as the time travel began, it ended, and they found themselves in the pocket dimension still.

**"Did it work?" Kurama asked.**

"We're going to have to wait to find out. We are both exhausted. What if we pop up in the middle of a battle?" Naruto asked.

And so they rested and waited for about 2 days.

"Do you feel energized, Kurama?" Naruto asked.

**"Yeah, lets go."** He responded.

Naruto used Kamui to take himself out of his dimension, and he was put right in the middle of a meeting with the Hokage discussing the Chunin exams.

When Naruto appeared, everyone in the room backed up and got defensive. Naruto looked down at his hands and feet and realized that he had the body of a 12 year old.

Kakashi was wide-eyed. "What are you doing here, Naruto? We are discussing important matters." Kakashi asked. However, Kakashi was not surprised because he got in the room, he got surprised with the way he did.

_That's the technique my Mangekyo Sharingan uses.._ Kakashi thought.

_Kurama, should I reveal myself?_ Naruto pondered.

**"You should, it will be a whole lot easier in the future if you do."** Kurama responded.

"I.. am not the Naruto you actually know. Keep this information among yourselves," Naruto started. "I am from the future, and in the future all of you guys die."

"Naruto, this better not be one of your pranks." Hiruzen said threateningly.

Naruto pulsed his Rinnegan. "I'm not pranking you. I am not the Naruto of this world; I came from the future."

Everyone in the room had their jaws drop to the floor when Naruto revealed his legendary dojutsu.

"Rinnegan.." Hiruzen said to himself. "What happened in the future to make you have to come back here?"

"Interdimensional creatures named the Otsutsuki. Someone who I thought was previously human brought back one of the most powerful dead members and destroyed the world," Naruto responded. "They had crazy, godlik- no, godly powers. They could teleport, rewrite time, make things out of nothing, anything you could think of, they could do."

Everyone

"And why do you have the Rinnegan?"

Naruto sighed, sadness in his eyes, "A friend gave it to me. I don't exactly know how to use it yet."

"You have told us a lot, but we still must have more confirmation. Is it okay if I have Inoichi go through your mind?"

"Sure."

Hiruzen called in Inoichi and had him go through his mind. As Inoichi put his hand on Naruto's head, all of the Jonin in the room looked curiously. Inoichi went wide eyed, and then he had an expression of empathy, and grief.

"He's Naruto," Inoichi declared. "and everything he said was true. Hiruzen, I need to talk to you in private after this.". Hiruzen nodded.

"Old man, can I stay in my genin team? I need to protect them, especially Sasuke." Naruto inquired.

"Why do you need to protect Sasuke the most?"

"He's the one who gave me the Rinnegan. He doesn't have it right now, but he will in the future. I also need to stop him from going down the path of hatred and revenge."

"Alright."

"I'm going to go now. I need to.. reminisce in old memories." Naruto walked out of the room and explored the tower again.

Naruto walked out of the Hokage tower and into the rest of the village. He looked around, breathing in the fresh air of the village for the first time in practically forever. After being stuck in that pocket dimension that smelled of sweat, blood, and tears, he began to appreciate Earth's air.

He spent some time outside just sitting down and looking at people. Sasuke walked past and looked at Naruto with interest.

"Naruto." Sasuke tried to get Naruto's attention.

Naruto's head snapped up to Sasuke. Tears welled up in his eyes and then he just ran away.

Sasuke looked at the direction he ran, then just shrugged and kept walking.

Naruto stopped in the middle of a forest and sat on a log. "I'm not ready to see him yet.." Naruto said.

**"Obviously you aren't. You've seen him die, and furthermore you even have a relic of his future."** Kurama responded.

Naruto sat there for a moment, regaining his confidence and just reminding himself that he needs to pull himself together. He finally stood up, and went to his apartment.

(Despite everything that happened, I'm going to actually stay true to canon and not have his apartment filled with graffiti and traps, because that's kind of stupid.)

When Naruto looked at himself in the mirror, he wondered how no one stared at hm. His clothes were really big and baggy on him, his hair was rough, dirty, and unkempt, and he was just dirty in general.

He hopped in the shower and cleaned himself up. He found his orange jumpsuit and put it on. He got into bed and went to sleep after a long, long day.


	2. Chapter 2

"The Chunin exams huh.." Naruto said to himself as he looked down at a piece of paper and walked down a street in the village. Naruto went to his apartment.

"I'm going to have to save the old man from Orochimaru, and I have to meet Ero-Sennin." Naruto said to himself. He ate some instant ramen and then left his apartment, going to the center of the village in order to look for Jiraiya.

_When I met Ero-Sennin it was at the Konoha Hot Springs, so I should check there first._ Naruto thought. He ran, rooftop to rooftop, to the Konoha Hot Springs, and found him peeking at the women's hot springs. He went and stood behind Jiraiya and tapped his shoulder.

Jiraiya jumped and stepped back. He looked left and right until he looked down and saw Naruto. "What are you doing, brat? You interrupted my research!" Jiraiya said.

"You were peeking on a hot spring so you can write your less than mediocre novel," Naruto quipped. "Anyways, I'm Naruto, if you couldn't tell already, and I need you to come with me."

"Why should I come with you, brat?"

"The old man and I have important things to tell you." Naruto responded and left it at that.

"Old man?" Jiraiya asked. "Hiruzen. Sandaime Hokage, your teacher." Naruto responded. Jiraiya nodded and began to walk in the direction of Konoha. Naruto followed.

"No need." Naruto said and used Kamui to teleport them both to Hiruzen's office. Jiraiya was shocked. Hiruzen looked at Naruto with surprise, and then his expression went back to normal, almost as if he was expecting that to happen.

"Okay Ero-Sennin-" Naruto started. "I'm not a pervert, I'm a super pervert!" Jiraiya interrupted. "I'm from the future, I have a Rinnegan, and there are a multitude of dangers in the future of this place." Naruto continued.

Jiraiya had to process what he said and then replied with, "Explain."

Naruto then explained everything that happened to Jiraiya and also Hiruzen who was listening in. From the invasion of Konoha to the reason why Naruto had to travel back in the first place.

"Wow.. you've been through a lot, huh?" Jiraiya said. "You need a hug?" he asked.

Naruto nodded and went up to hug Jiraiya. Naruto stepped away from the hug after a while. "Old man, can you oversee me and Ero-Sennin spar?" He asked. Hiruzen nodded and led them to a private training ground.

Hiruzen stood at the sidelines and Naruto and Jiraiya stood facing each other. Naruto ran towards Jiraiya. He faked a right hook and then tried to do a roundhouse kick to the left side of his head. Jiraiya blocked the kick with his forearm, grabbed him by the ankle, and then threw him. Naruto twisted in the air and then landed on his feet.

Naruto spawned in 5 shadow clones. They all rushed Jiraiya, coming in with a flurry of punches and kicks. One clone managed to land a hit on Jiraiya's jaw. Jiraiya then punched every clone and dispelled them.

"I guess its time to raise it up a notch. I forgot how powerful you are." Naruto said. Naruto made one clone. Naruto and his clone ran towards Jiraiya. Jiraiya kicked away Naruto and his clone at the same time, making the clone dispel. While using the clone's smoke as a screen, he threw a kunai at Jiraiya's calf so fast that he nicked his calf before he could even react.

"Was that it, brat?" Jiraiya quipped. Naruto simply pointed behind Jiraiya.

There was the original Naruto midway through a roundhouse kick to his right jaw. His foot made contact with his face, and it made Jiraiya get knocked back around 10 feet.

"That was a good kick, brat, I'll give you that. But that's not enough." Jiraiya said.

Naruto charged up a low-powered Rasengan and made another clone which also had a low-powered Rasengan. The clone backed up a bit, before they both ran towards each other, with their Rasengan out.

Jiraiya was curious as to what they were doing until Naruto's Rinnegan pulsed and he found himself in between the two Narutos, pinched in between two balls of energy. When the two Rasengan dissipated and the clone dispelled, Naruto grabbed Jiraiya and threw him.

"That was a good strategy. Did you use your Rinnegan?" Jiraiya asked.

"Yeah, I saw Sasuke do that switching move a bunch of times. When me and my clone charged at each other with Rasengan, that was actually a copy of the first strategy Sasuke used with his Rinnegan." Naruto said with a bit of a sad smile.

Jiraiya powered up a Rasengan and charged at Naruto, faking a left punch, then going for a left kick which hit Naruto. He then finished the combo with his Rasengan in his right hand.

Naruto saw the Rasengan go to him very slowly. His Mangekyo Sharingan activated, and out of instinct, he made the Rasengan become intangible; making it impossible for it to affect him (1). He jumped back and looked down at his hands, his face crestfallen.

"What's wrong, brat?" Jiraiya asked.

"I've been severely weakened. It's like I'm a teenager again," Naruto said with a comically sad voice. "It's going to take forever to get back to my regular strength!" He slouched and became depressed, Hashirama-style. Almost as quickly his depression came, he bounced back, becoming happy again.

"You're still extremely powerful. I can tell you're holding back. You also just used a technique from your Mangekyo Sharingan, so it seems like you're going to grow past your past strength." Jiraiya said to Naruto helpfully.

Naruto smiled and said, "Thanks.. Ero-Sennin!"

Jiraiya became irritated and rushed Naruto again, wielding dual Rasengan in both of his palms. Naruto loosened up a bit and dodged Jiraiya's blows with more ease, flowing past his strikes and countering them with his own. Naruto broke out of the exchange and jumped back once again, changing his stance.

He jumped to a tree and broke off a branch, using his chakra to mold it into a bo-staff. He spread his legs far apart, almost looking like he was halfway between doing the splits and just standing regularly. His right arm (which was holding the staff) far back, and his left arm having a Rasengan ready.

"I've never seen that stance before, what is that called?" Jiraiya asked.

"Hmm.. I've never gave it a name.. I'll call it the Naruto style!" Naruto declared with a smile. Jiraiya chuckled. "Now, if I was actually going all out, I would have my actual bo-staff, which is made of a material that disintegrates anything on contact."

Jiraiya's face blanched at that statement. He was glad he wasn't his enemy.

Naruto charged at Jiraiya, jabbing him in the stomach with his bo-staff at an almost un-shinobi-like speed. Jiraiya was taken aback by the jab; he saw it before he felt it. Naruto then kicked him in the chest, and knocked him back around 20 feet. He followed up by incorporating wind chakra into his Rasengan and turning it into a Rasenshuriken. He threw it at Jiraiya.

"I concede!" Jiraiya said. Naruto quickly dispelled his Rasenshuriken. He walked up to Jiraiya and helped him up. "You're powerful, brat. You could probably take on all three of us and win."

Naruto smiled and scratched the back of his head and thanked him.

"I have the Chunin exams in a month, by the way." Naruto said.

"What? You're too powerful to be in the exams!" Jiraiya said.

"Don't worry, Ero-Sennin. The old-man and I have agreed to simply manipulate some aspects of the exam, and I'm only going to fight certain people, not fresh Genin."

Jiraiya seemed to have calmed down at that statement.

****"Naruto, something terrible has happened."**** Naruto was pulled into his mindscape. "What happened, Kurama?"

****"We've never discussed what happened with our past counterparts. And because of that, the Akatsuki has my past self."****

"Damn.. how many tailed beasts do they have right now?"

****"None, they only have your past body. They have to absorb everyone else before they get us."****

Naruto sighed in relief. "Well that's good. I need to regain my powers again; most of my ability was lost when I used that seal." he chuckled and scratched the back of his head. He then left his mindscape.

Jiraiya and Hiruzen gave him questioning looks. "Oh, I spaced out for a bit because I was talking to Kurama. Apparently the Akatsuki has taken my past counterpart away." Naruto said.

"We should go and find your past counterpart then." Hiruzen said.

"No, its fine. Due to certain logic, when I came into this timeline I actually replaced/killed my old self, the only thing left there is a body. And besides, they have to look for the rest of the tailed beasts before they can do anything with my old body. We still have a month before the Chunin exams begin, correct?"

Hiruzen nodded.

"Okay, for this whole month I will train." Naruto said. And he walked off to his apartment, getting ready for the next day of his training month. 

****(1) Since Obito's intangibility is based off of how he can use Kamui on himself to just transport certain parts of his body so that they are technically not 'there', Naruto does the same, just at a distance.****


	3. Chapter 3

It was mid-day. Naruto was working on his Six-paths senjutsu, trying to make the cloak last longer.

Until, all of a sudden, a black portal ripped a whole through space and time, and Naruto saw it. Out of it came an Otsutsuki clan member donning the white cloak and all. Oddly enough, he had Minato's hairstyle, minus the headband.

When he came out of the portal, Naruto automatically tensed up and got into a battle stance.

The Otsutsuki put his hands up and said, "Chill out. I'm not here to fight. I need to tell you and give you stuff."

"First of all, my name is Minato Namikaze. As it turns out, people sealed with the Shiki seal become Otsutsuki clan members. We are constructs of chakra, like tailed beasts." He continued.

Naruto snarled, "Don't you dare try to impersonate my father!"

"Do you need proof? You can even ask me something out your past-er future. The clan I'm in transcends the limitations of time, so if you time travel some of us aren't affected.

"Yeah. Who was Sasuke? How did you meet me?"

"Sasuke, at one point, used to be your rival. Then he left for Orochimaru and betrayed the village. At the Fourth Great Shinobi War, he helped seal Kaguya into a new moon. I met you twice, actually. Once during the Fourth Great Shinobi War, and when you almost released the Kyubi to defeat Pein."

"Wow, you actually are my dad." Naruto ran up to him and hugged him. "Was that all you needed to tell me?"

"No. I have one more thing, " Minato's face became solemn. "The Otsutsuki you were fighting may come into this dimension in the next 6 years or so, so you have to prepare. You couldn't even scratch him with your previous strength, so that is why I must give you something; my chakra. If I even give you a little bit your body will feed off of it and begin to make more of the chakra I gave you. Expect some changes to your body. Like better reflexes. Better than the reflexes you have in your strongest form. More strength. All of your techniques are amplified."

"Wait, wait. To stop that idiot Otsutsuki from destroying the world, you're going to give me some of your chakra?"

"Yes." Minato raised his hand, and before Naruto could say another word, gargantuan amounts of chakra flew out of his palm and began to flow into Naruto's stomach and head.

Naruto passed out. Minato dropped a scroll next to Naruto and left the dimension.

Naruto woke up in his mindscape. As he walked down the halls, instead of just finding one room, he saw two. The new room had a ball with the kanji for 20 on it. It was pure white, with streams of its energy getting fed into the pipes he had in his mindscape.

"Wow.." was all Naruto could say. He could feel the otherworldly power course through him. He was jolted awake as he saw Kakashi, Sakura, and Sasuke stare at him. The former two comrades with an actual face of concern, while the latter comrade looked at Naruto while hiding his concern.

"Naruto!" Sakura said first as she went down to hug him.

"You were out for almost a whole month, Naruto, and the Chunin exams are tomorrow. You can drop out if you're too weak to do so." Kakashi informed Naruto.

"No, I won't. I have numerous things to do; too much to just quit now." Naruto said as he gave Kakashi a knowing look.

"Alright, we will do one last team exercise before tomorrow's Chunin Exams." Kakashi said. Naruto got up and followed the team to their training ground.

"Okay, we will just spar." Kakashi declared. "Naruto vs Sasuke."

Naruto and Sasuke stood facing each other in a chalk-lined circle. "Try not to lose too easily, idiot." Sasuke taunted Naruto.

Naruto simply smirked.

Sasuke ran at Naruto. He went for a right punch but Naruto blocked it and countered with a punch that went directly into Sasuke's stomach. The punch knocked Sasuke out of the ring.

"Naruto wins. Sakura you're up next."

Sakura, with a little bit of hesitation, walked into the ring. Kakashi told them to start. Right as Kakashi said start, Naruto went up to Sakura and pushed her out of the ring.

"Alright.. I'm up." Kakashi said.

"Get ready to lose, idiot. You got lucky against me." Sasuke said.

The match started and the two opponents just stood there and sized each other up. All of a sudden, Kakashi heard a voice behind him that said, "I could've won.". He turned around and saw the tip of a kunai in his face. Kakashi pushed him out of the ring.

As Naruto was falling, he threw a kunai and replaced himself with the kunai.

"Shinra Tensei!" Naruto used one of his Rinnegan jutsu to push Kakashi out of the ring. "I win!" Naruto said, smiling. Sasuke and Sakura stood there, horrified. They saw Naruto's Rinnegan.

"Rinnegan.." Sasuke said. "HOW DO YOU HAVE THOSE EYES?"

"They're... a transplant." Naruto said. He picked up his kunai and jumped when he saw that his Rinnegan changed. They were red, with 12 tomoe.

****"Your eye is evolving into a Tengan." ****

_Another dojutsu? I didn't even get the chance to learn how to use the Rinnegan yet.._

****"You should be grateful. Also, you're not going to lose your Rinnegan, just your other eye."****

_My Sharingan? Noooo! _

****"Yes, but your Rinnegan already has your Sharingan powers, so you're fine."**** Naruto was pulled into his mindscape once again. His mindscape looked different. It was a plain that went far into the horizon. There was nothing but grass and a couple of trees.

****"If you're wondering why your mindscape looks so different, its because the chakra you've received has affected your mind. You can stay calm easier now. The chakra also had information in it which I picked up."****

****"First of all, that chakra is going to obviously affect your eyes. I don't know what powers the Tengan has, but since it is only created by putting pure Otsutsuki chakra into an earthly being such as yourself, it is most likely extremely powerful; more so than the Rinnegan."****

"Wow.. why do YOU look different Kurama?" Naruto asked. He was right, Kurama did look a little different.

Kurama's fur was a few shades darker, and he had ten tails instead of nine.

****"I absorbed some of the chakra on accident."**** Kurama replied.****"Anyways, this chakra will make you even stronger than my father."****

Naruto's jaw went slack at that statement. He would be stronger than the Sage?

****"Your reflexes would be godlike, your strength would be godlike, everything about you will be godlike in the next couple of days or so. Also, your chakra reserves are almost as much as back when I had nine tails. Anyways, goodbye, I'm going to take a nap."**** And just like that, Kurama pushed Naruto out of his mindscape.

"Why did you space out like that, Naruto?" Sakura asked.

_Should I tell them about you?_ Naruto asked Kurama.

****"Yes, you might as well reveal everything right now."****

"I was talking with Kurama." Naruto said.

"Kurama?" Sakura and Sasuke asked at the same time. Naruto then went and explained everything that happened, telling them not to tell anyone several times along the way.

"Wow.. That explains that rampage you had at the bridge." Sakura said.

"So you're basically a god now?" Sasuke asked.

"No, and I never will be, luckily," Naruto responded. "being a god would suck because you have no imperfections, and imperfections make life fun."

"Anyways, since that Otsutsuki god will be here in a couple of years, I have to train in order to protect you guys." Naruto continued.

"We have to train to protect everyone else." Sasuke corrected Naruto with a small smile. Naruto grinned. "Good. We can talk about this later, but now, we have to focus on saving the Hokage.."


End file.
